An owner of a troubled Brooklyn pharmacy linked to an NYPD steroid scandal fatally shot himself last night, leaving a note begging his wife’s forgiveness, authorities said.

John Rossi, 56, of Lowen’s Pharmacy in Bay Ridge, was found slumped on the floor near his son-in-law’s desk in a second-floor office over the store at 7 p.m.

He had shot himself once in the head, sources said. A .380-caliber handgun was still in his hand.

A bottle of Johnnie Walker whiskey, Valium and a can of Coca-Cola were on the desk along with a note to his wife, Justine:

” ‘Please forgive me,’ ” the note begged, an investigator said.

His wife “was screaming, hysterical” when she arrived at the pharmacy, according to the investigator.

She and her son-in-law Edward Letendre – whose wife, Kristen, Rossi’s daughter, gave birth early yesterday – were whisked away by cops.

Lowen’s was raided last May, when medical records and millions of dollars worth of performance-enhancing drugs were seized.

Police sources said prescriptions were filled there by several cops. Using steroids violates NYPD policy.

Rossi “was a different person after that,” said customer Barbara Rosentreter. “You could see the worry in his face.”

Five cops failed subsequent tests and face departmental charges, a source said. Rossi had not been charged.

The raid was part of a wide-ranging probe by Albany DA David Soares into illegal prescription-drug sales that allegedly involved a slew of major-league ballplayers, including former Yankee stars Roger Clemens and Andy Pettitte.

The probe targeted steroid suppliers.

The Lowen’s raid in May – and another in October – were mentioned in last month’s bombshell Mitchell report, which documented the use of steroids in Major League Baseball.